[gmx-users] Re: 2. protein in dppc (edmund lee)

[Gerrit Groenhof]

Hi,

If I am allowed to do some advertisement:

you could try the tool g_membed  for inserting proteins as well

http://wwwuser.gwdg.de/~ggroenh/membed.html

Gerrit

gmx-users-request at gromacs.org wrote:
>    2. protein in dppc (edmund lee)
>
> Date: Tue, 23 Feb 2010 15:55:36 +0800
> From: edmund lee <eyemnoob2008 at hotmail.com>
> Subject: [gmx-users] protein in dppc
> To: <gmx-users at gromacs.org>
> Message-ID: <SNT122-W306118246354907DD2561EDD420 at phx.gbl>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear Justin and all..
> I have been struggled for the pass few weeks...I follow the KALP-15 in DPPC tutorials but I am using my own protein instead.
> I had successfully reached the step INFLATEGRO where 2 lipid removed from the upper layer n 2 lipids removed from the lower layer. Then i updated my topology with deducted 4 number of molecule of lipid.
> then I generated the strong_porse.itp using the following command:
> genrestr -f 1_newbox.gro -o strong_posre.itp -fc 100000 100000 100000
> here is how the strong_posre.itp file look like[ position_restraints ];  i funct       fcx        fcy        fcz   1    1     100000     100000     100000   2    1     100000     100000     100000   3    1     100000     100000     100000   4    1     100000     100000     100000   5    1     100000     100000     100000................3483    1     100000     100000     1000003484    1     100000     100000     1000003485    1     100000     100000     1000003486    1     100000     100000     100000
> then i updated the topology (as shown below)
> ; Include Position restraint file#ifdef POSRES#include "posre.itp"#endif
> ; Strong position restraints for InflateGRO#ifdef STRONG_POSRES#include "strong_posre.itp"#endif
> ; Include DPPC chain topology#include "dppc.itp"
> ; Include water topology#include "spc.itp"
> ; System specifications[ system ]128-Lipid DPPC Bilayer 
> [ molecules ]; molecule name nr.DPP            124SOL           3655
>
>
>
> and I also add in the "define" line in the energyminimization.mdp file
> here is my em.mdp file 
> define                   =-DSTRONG_POSRESintegrator             = steepnsteps                   = 200constraints            = noneemtol                    = 1000.0nstcgsteep            = 10 ; do a steep every 10 steps of cgemstep                 = 0.01 ; used with steepnstcomm              = 1coulombtype        = PMEns_type                = gridrlist                       = 1.0rcoulomb              = 1.0rvdw                     = 1.4Tcoupl                  = noPcoupl                  = nogen_vel                = nonstxout                 = 0 ; write coords every # stepoptimize_fft          = yes
>
> HOWEVER, I get this error when I proceed to the grompp step.
> Fatal error:Syntax error - File strong_posre.itp, line 3Last line read:'[ position_restraints ]'Invalid order for directive position_restraints
> Can anyone guide me in this?Yr comments and advices are appreciated.
> best regards
> edmund 		 	   		  
> _________________________________________________________________
>